rename all .atoms properties to .frames (#349)

* rename all `.atoms` properties to `.frames`

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* remove ReadData node

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* rename some more .atoms to .frames

* update some more tests

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* fix test?

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

ipsuite/__init__.pyi

@@ -89,7 +89,7 @@ from .configuration_selection import (
 )
 
 # Data
-from .data_loading import AddData, AddDataH5MD, ReadData
+from .data_loading import AddData, AddDataH5MD
 
 # Datasets
 from .datasets import MD22Dataset
@@ -131,7 +131,6 @@ __all__ = [
     # Data
     "AddData",
     "AddDataH5MD",
-    "ReadData",
     # Datasets
     "MD22Dataset",
     # Bootstrap

ipsuite/analysis/bond_stretch.py

@@ -67,7 +67,7 @@ def run(self):
         e_uncertainties = []
         f_uncertainties = []
 
-        self.atoms = []
+        self.frames = []
         for i in range(self.n_steps):
             struct.set_distance(self.idxs[0], self.idxs[1], bond_lengths[i], mask=mask)
             ens_energies.append(struct.get_total_energy())
@@ -77,7 +77,7 @@ def run(self):
             if "forces_uncertainty" in struct.calc.results:
                 f_uncertainties.append(struct.calc.results.get("forces_uncertainty"))
 
-            self.atoms.append(struct.copy())
+            self.frames.append(struct.copy())
 
         results = {
             "energy": np.asarray(ens_energies),

ipsuite/analysis/model/dynamics.py

@@ -81,13 +81,13 @@ def run(self):
 
         energies = []
 
-        self.atoms = []
+        self.frames = []
 
         for stdev in tqdm.tqdm(stdev_space, ncols=70):
             atoms.positions = reference.positions
             atoms.rattle(stdev=stdev, seed=self.seed)
             energies.append(atoms.get_potential_energy())
-            self.atoms.append(freeze_copy_atoms(atoms))
+            self.frames.append(freeze_copy_atoms(atoms))
 
         self.energies = pd.DataFrame({"y": energies, "x": stdev_space})
 
@@ -134,7 +134,7 @@ def run(self):
         original_atoms.calc = self.model.get_calculator(directory=self.model_outs)
 
         energies = []
-        self.atoms = []
+        self.frames = []
         if self.mapping is None:
             scaling_atoms = original_atoms
         else:
@@ -151,15 +151,15 @@ def run(self):
                 eval_atoms.calc = original_atoms.calc
 
             energies.append(eval_atoms.get_potential_energy())
-            self.atoms.append(freeze_copy_atoms(eval_atoms))
+            self.frames.append(freeze_copy_atoms(eval_atoms))
 
         self.energies = pd.DataFrame({"y": energies, "x": scale_space})
 
-        if "energy_uncertainty" in self.atoms[0].calc.results:
+        if "energy_uncertainty" in self.frames[0].calc.results:
             fig, ax, _ = plot_with_uncertainty(
                 {
                     "std": np.std(
-                        [a.calc.results["energy_uncertainty"] for a in self.atoms]
+                        [a.calc.results["energy_uncertainty"] for a in self.frames]
                     ),
                     "mean": self.energies["y"],
                 },
@@ -246,7 +246,7 @@ def run(self):
         temperature, total_energy = utils.ase_sim.get_energy(atoms)
 
         energy = []
-        self.atoms = []
+        self.frames = []
 
         with tqdm.trange(
             self.steps,
@@ -269,7 +269,7 @@ def run(self):
                         f" {self.max_temperature} K. Simulation was stopped."
                     )
                     break
-                self.atoms.append(freeze_copy_atoms(atoms))
+                self.frames.append(freeze_copy_atoms(atoms))
 
         self.flux_data = pd.DataFrame(
             energy, columns=["meassured_temp", "energy", "set_temp"]
@@ -375,7 +375,7 @@ class MDStability(base.IPSNode):
     stable_steps_df: pd.DataFrame = zntrack.plots()
 
     @property
-    def atoms(self) -> typing.List[ase.Atoms]:
+    def frames(self) -> typing.List[ase.Atoms]:
         with self.state.fs.open(self.traj_file, "rb") as f:
             with h5py.File(f) as file:
                 return znh5md.IO(file_handle=file)[:]

ipsuite/analysis/model/predict.py

@@ -40,7 +40,7 @@ class Prediction(base.ProcessAtoms):
     model: models.MLModel = zntrack.deps()
 
     def run(self):
-        self.atoms = []
+        self.frames = []
         calc = self.model.get_calculator()
 
         for configuration in tqdm.tqdm(self.get_data(), ncols=70):
@@ -58,7 +58,7 @@ def run(self):
                 ):  # required for nequip, GAP
                     pass
 
-            self.atoms.append(freeze_copy_atoms(atoms))
+            self.frames.append(freeze_copy_atoms(atoms))
 
 
 class PredictionMetrics(base.ComparePredictions):

ipsuite/analysis/sensitivity.py

@@ -139,8 +139,6 @@ def get_values(self, data, item):
     def run(self):
         values = []
 
-        self.data = [x.atoms if isinstance(x, zntrack.Node) else x for x in self.data]
-
         for atoms, sim in zip(self.data, self.sim_list):
             radius = sim.constraints[0].radius
             atom_id = sim.constraints[0].get_selected_atom_id(atoms[0])

ipsuite/base/base.py

@@ -19,13 +19,13 @@ class ProcessAtoms(IPSNode):
     ----------
     data: list[ase.Atoms]
         The atoms data to process. This must be an input to the Node
-    atoms: list[ase.Atoms]
+    frames: list[ase.Atoms]
         The processed atoms data. This is an output of the Node.
         It does not have to be 'field.Atoms' but can also be e.g. a 'property'.
     """
 
     data: list[ase.Atoms] = zntrack.deps()
-    atoms: list[ase.Atoms] = fields.Atoms()
+    frames: list[ase.Atoms] = fields.Atoms()
 
     def get_data(self) -> list[ase.Atoms]:
         """Get the atoms data to process."""
@@ -47,7 +47,7 @@ class ProcessSingleAtom(IPSNode):
     data_id: int | None
         The id of the atoms object to process. If None, the first
         atoms object is used. Only relevant if 'data' is a list.
-    atoms: list[ase.Atoms]
+    frames: list[ase.Atoms]
         The processed atoms data. This is an output of the Node.
         It does not have to be 'field.Atoms' but can also be e.g. a 'property'.
         Although, we only process a single atoms object, we return a list.
@@ -58,7 +58,7 @@ class ProcessSingleAtom(IPSNode):
     data: typing.List[ase.Atoms] = zntrack.deps()
     data_id: int = zntrack.params(-1)
 
-    atoms: typing.List[ase.Atoms] = fields.Atoms()
+    frames: typing.List[ase.Atoms] = fields.Atoms()
 
     def get_data(self) -> ase.Atoms:
         """Get the atoms object to process given the 'data' and 'data_id'.
@@ -129,4 +129,4 @@ class Flatten(ProcessAtoms):
     """Flattens list[list[ase.Atoms]] to list[ase.Atoms]"""
 
     def run(self):
-        self.atoms = sum(self.data, [])
+        self.frames = sum(self.data, [])

ipsuite/base/protocol.py

@@ -9,7 +9,7 @@
 class HasAtoms(typing.Protocol):
     """Protocol for objects that have an atoms attribute."""
 
-    atoms: list[ase.Atoms]
+    frames: list[ase.Atoms]
 
 
 class HasSelectedConfigurations(typing.Protocol):
@@ -30,7 +30,7 @@ class ProcessAtoms(typing.Protocol):
     """
 
     data: list[ase.Atoms]
-    atoms: list[ase.Atoms]
+    frames: list[ase.Atoms]
 
 
 # Collection of complex type hints

ipsuite/bootstrap/random_displacements.py

@@ -53,13 +53,13 @@ def run(self) -> None:
         (self.model_outs / "outs.txt").write_text("Lorem Ipsum")
         if self.model is not None:
             calculator = self.model.get_calculator(directory=self.model_outs)
-            self.atoms = []
+            self.frames = []
             for atoms in tqdm.tqdm(atoms_list, ncols=120, desc="Applying model"):
                 atoms.calc = calculator
                 atoms.get_potential_energy()
-                self.atoms.append(freeze_copy_atoms(atoms))
+                self.frames.append(freeze_copy_atoms(atoms))
         else:
-            self.atoms = atoms_list
+            self.frames = atoms_list
 
     def bootstrap_configs(sefl, atoms: ase.Atoms, rng):
         raise NotImplementedError
@@ -101,7 +101,7 @@ def bootstrap_configs(self, atoms, rng):
         else:
             atoms_list = []
 
-        mapping = ips.geometry.BarycenterMapping()
+        mapping = ips.BarycenterMapping()
 
         _, molecules = mapping.forward_mapping(atoms)
         for _ in range(self.n_configurations):
@@ -139,7 +139,7 @@ def bootstrap_configs(self, atoms, rng):
         if self.maximum > 2 * np.pi:
             log.warning("Setting maximum to 2 Pi.")
 
-        mapping = ips.geometry.BarycenterMapping()
+        mapping = ips.BarycenterMapping()
 
         _, molecules = mapping.forward_mapping(atoms.copy())
         for _ in range(self.n_configurations):

ipsuite/bootstrap/surface_mods.py

@@ -102,7 +102,7 @@ def run(self) -> None:
                     )
                     atoms_list[-1].extend(extension)
 
-        self.atoms = atoms_list
+        self.frames = atoms_list
 
 
 class SurfaceRasterMetrics(analysis.PredictionMetrics):

ipsuite/calculators/ase_geoopt.py

@@ -95,7 +95,7 @@ def get_atoms(self) -> ase.Atoms:
         return atoms
 
     @property
-    def atoms(self) -> typing.List[ase.Atoms]:
+    def frames(self) -> typing.List[ase.Atoms]:
         with self.state.fs.open(self.traj_file, "rb") as f:
             with h5py.File(f) as file:
                 return znh5md.IO(file_handle=file)[:]

ipsuite/calculators/ase_md.py

@@ -582,7 +582,7 @@ def get_atoms(self, method="run") -> ase.Atoms | typing.List[ase.Atoms]:
             return atoms
 
     @property
-    def atoms(self) -> typing.List[ase.Atoms]:
+    def frames(self) -> typing.List[ase.Atoms]:
         with self.state.fs.open(self.traj_file, "rb") as f:
             with h5py.File(f) as file:
                 return znh5md.IO(file_handle=file)[:]
@@ -727,7 +727,7 @@ def map(self):  # noqa: A003
         for atoms in structures:
             metrics, current_step = self.run_md(atoms=atoms)
             metrics_list.append(metrics)
-            self.structures.append(self.atoms[-current_step:])
+            self.structures.append(self.frames[-current_step:])
 
         # Flatten metrics dictionary
         flattened_metrics = {}

ipsuite/calculators/cp2k.py

@@ -146,7 +146,7 @@ def _run_cp2k(self, atoms, cp2k_input_script):
             raise RuntimeError(f"CP2K failed with return code {proc.returncode}:")
 
     @property
-    def atoms(self):
+    def frames(self):
         """Return the atoms object."""
         # TODO this is for single point, what about MD
         data = {}
@@ -217,7 +217,7 @@ def run(self):
             file.unlink()
 
     @property
-    def atoms(self) -> typing.List[ase.Atoms]:
+    def frames(self) -> typing.List[ase.Atoms]:
         with self.state.fs.open(self.output_file, "rb") as f:
             with h5py.File(f) as file:
                 return znh5md.IO(file_handle=file)[:]

ipsuite/calculators/lammps.py

@@ -181,6 +181,6 @@ def get_template(
             yaml.dump({"sim_parameters": params}, file)
 
     @property
-    def atoms(self) -> list[ase.Atoms]:
+    def frames(self) -> list[ase.Atoms]:
         with self.state.fs.open(self.dump_file, mode="r") as file:
             return list(ase.io.iread(file, format="lammps-dump-text"))

ipsuite/calculators/orca.py

@@ -27,7 +27,7 @@ def run(self):
             db.append(atoms)
 
     @property
-    def atoms(self):
+    def frames(self):
         with self.state.fs.open(self.output_file, "rb") as f:
             with h5py.File(f) as file:
                 return znh5md.IO(file_handle=file)[:]

ipsuite/calculators/xtb.py

@@ -21,14 +21,14 @@ class xTBSinglePoint(base.ProcessAtoms):
     method: str = zntrack.params("GFN1-xTB")
 
     def run(self):
-        self.atoms = []
+        self.frames = []
 
         calculator = self.get_calculator()
 
         for atom in tqdm.tqdm(self.get_data(), ncols=70):
             atom.calc = calculator
             atom.get_potential_energy()
-            self.atoms.append(freeze_copy_atoms(atom))
+            self.frames.append(freeze_copy_atoms(atom))
 
     def get_calculator(self, **kwargs):
         """Get an xtb ase calculator."""

ipsuite/configuration_generation/gmx.py

@@ -344,7 +344,7 @@ def __post_init__(self):
         self.mdp_files = [pathlib.Path(mdp_file) for mdp_file in self.mdp_files]
 
     @property
-    def atoms(self):
+    def frames(self):
         with self.state.fs.open(self.traj_file, "rb") as f:
             with h5py.File(f) as file:
                 return znh5md.IO(file_handle=file)[:]

ipsuite/configuration_generation/packmol.py

@@ -48,7 +48,7 @@ class Packmol(base.IPSNode):
     box: list = zntrack.params(None)
     density: float = zntrack.params(None)
     structures: pathlib.Path = zntrack.outs_path(zntrack.nwd / "packmol")
-    atoms: list[ase.Atoms] = fields.Atoms()
+    frames: list[ase.Atoms] = fields.Atoms()
     pbc: bool = zntrack.params(True)
 
     def __post_init__(self):
@@ -96,15 +96,15 @@ def run(self):
         if self.pbc:
             atoms.cell = self.box
             atoms.pbc = True
-        self.atoms = [atoms]
+        self.frames = [atoms]
 
     def _get_box_from_molar_volume(self):
         """Get the box size from the molar volume"""
         self.box = get_box_from_density(self.data, self.count, self.density)
         log.info(f"estimated box size: {self.box}")
 
     def view(self) -> view:
-        return view(self.atoms, viewer="x3d")
+        return view(self.frames, viewer="x3d")
 
 
 class MultiPackmol(Packmol):
@@ -145,7 +145,7 @@ class MultiPackmol(Packmol):
 
     def run(self):
         np.random.seed(self.seed)
-        self.atoms = []
+        self.frames = []
 
         if self.density is not None:
             self._get_box_from_molar_volume()
@@ -187,4 +187,4 @@ def run(self):
                 atoms.cell = self.box
                 atoms.pbc = True
 
-            self.atoms.append(atoms)
+            self.frames.append(atoms)

ipsuite/configuration_generation/smiles_to_atoms.py

@@ -45,7 +45,7 @@ def view(self) -> view:
 
 
 class SmilesToConformers(base.IPSNode):
-    atoms: list[ase.Atoms] = fields.Atoms()
+    frames: list[ase.Atoms] = fields.Atoms()
 
     smiles: str = zntrack.params()
     numConfs: int = zntrack.params()
@@ -62,7 +62,7 @@ def run(self):
             randomSeed=self.seed,
             maxAttempts=self.maxAttempts,
         )
-        self.atoms = []
+        self.frames = []
         for conf in mol.GetConformers():
             atoms = ase.Atoms(
                 positions=conf.GetPositions(),
@@ -74,4 +74,4 @@ def run(self):
                 atoms.set_cell([self.cell, self.cell, self.cell])
                 atoms.center()
 
-            self.atoms.append(atoms)
+            self.frames.append(atoms)